yes, you symlinked it to itself which is why you are getting the infinite recursion error. You need to delete /usr/local/freesurfer/subjects/fsaverage
and download the fsaverage dir again, put it in that directory, then symlink from your /mnt/hgfs/mydata/fsaverage to /usr/local/freesurfer/subjects/fsaverage
cheers Bruce On Fri, 19 Sep 2014, Mahmoud wrote:
Bruce,
I already had my data in a shared folder (/mnt/hgfs/mydata) but I got the permission error the same point that I got the symlink error lastly. So, I tought that might be due to something related to shared directory. Then I copied my subjects under the $SUBJECTS_DIR but got the symlink error.
running ls -l /usr/local/freesurfer/subjects /fsaverage shows me this:
lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23 /usr/local/freesurfer/subjects/fsaverage -> /usr/local/freesurfer/subjects/fsaverage
Thank you, Mahmoud
On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: the directory /usr/local/freesurfer/subjects is for subjects that we distribute and NOT where you should be putting your subject data. Is that what you are doing? You may have overwritten the fsaverage dir there. Can you run:
ls -l /usr/local/freesurfer/subjects/fsaverage and send us the results? you should create a directory elsewhere with your subject data and point SUBJECTS_DIR at it cheers Bruce On Fri, 19 Sep 2014, Mahmoud wrote: Bruce, Here is the info when I open a new terminal: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni ubuntu:~> On Fri, Sep 19, 2014 at 8:56 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you tell us what your FREESURFER_HOME is and what your SUBJECTS_DIR is? You will need to remove the broken link probably On Fri, 19 Sep 2014, Mahmoud wrote: Hi Bruce, Actually I couldn't. It says: ls: cannot access /usr/local/freesurfer/subjects/fsaverage: Too many levels of symbolic links And even I couldn't cd to fsaverage ! In fact there is no directory under SUBJETCS_DIR named fsaverage, it seems the fsaverage under SUBJETCS_DIR is just a broken link, and I have no idea why the the link is broken and how to fix it. Any help would be highly appreciated ! Thank you, Mahmoud On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mahmoud were you able to create a symlink to fsaverage in your SUBJECTS_DIR? If not, that is the reason for this error Bruce On Thu, 18 Sep 2014, Mahmoud wrote: Dear all, After running "recon-all -i $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm -subject case018_tp2 -all" I'm always getting the following error and really don't know how to fix. Could anybody please help me. The recon-all.log file is attached. Thank you, Mahmoud Reporting on 70 segmentations mri_segstats done /usr/local/freesurfer/subjects/case018_tp2/label #-------------------------------------------- #@# BA Labels lh Thu Sep 18 20:23:27 EDT 2014 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /usr/local/freesurfer/subjects; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject case018_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = case018_tp2 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux ubuntu 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s case018_tp2 exited with ERRORS at Thu Sep 18 20:23:27 EDT 2014 For more details, see the log file /usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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